5B87

Crystal structure of a Cysteine Desulfurase from Thermococcus onnurineus NA1 in complex with alanine at 2.3 Angstrom resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5B7S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	0.03 M MgCl2, 0.03 M CaCl2, 15% (v/v) glycerol, 15% (w/v) PEG 4000, 5mM L-alanine, 1mM PLP and 0.1 M Tris (base)/ Bicine pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.282	α = 90
b = 93.809	β = 90
c = 145.534	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2014-07-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.97	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.28	50	95.5	0.095	34.6	6.4		40955

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.28	2.32	100		0.38	5.3	6.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5B7S	2.28	49.4	38845	2040	95.9	0.185	0.183	0.232	RANDOM	43.09

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.25			4.47		-4.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.107
r_dihedral_angle_3_deg	20.714
r_dihedral_angle_4_deg	15.378
r_long_range_B_other	8.405
r_long_range_B_refined	8.404
r_dihedral_angle_1_deg	6.897
r_scangle_other	6.809
r_mcangle_it	4.91
r_mcangle_other	4.91
r_scbond_other	4.48
r_scbond_it	4.479
r_mcbond_it	3.452
r_mcbond_other	3.451
r_angle_refined_deg	2.03
r_angle_other_deg	1.246
r_chiral_restr	0.161
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6218
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing